Summary of study ST000899

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000625. The data can be accessed directly via it's Project DOI: 10.21228/M8W983 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000899
Study TitleAlterations in Lipid, Amino Acid, and Energy Metabolism Distinguish Crohn Disease from Ulcerative Colitis and Control Subjects by Serum Metabolomic Profiling
Study SummaryNon-invasive biomarkers are needed in inflammatory bowel disease (IBD) to help define disease activity and identify underlying pathogenic mechanisms. We hypothesized that serum metabolomics, which produces unique metabolite profiles, can aid in this search. The aim of this study was to characterize serum metabolomic profiles in patients with IBD, and to assess for differences between patients with ulcerative colitis (UC), Crohn disease (CD), and non-IBD subjects. Serum samples from 20 UC, 20 CD, and 20 non-IBD control subjects were obtained along with patient characteristics, including medication use and clinical disease activity. Non-targeted metabolomic profiling was performed using ultra-high performance liquid chromatography/mass spectrometry (UPLC-MS/MS) optimized for basic or acidic species and hydrophilic interaction liquid chromatography (HILIC/UPLC-MS/MS).
Institute
Vanderbilt University Medical Center
Last NameScoville
First NameElizabeth
Address1030C MRB IV, 2215 Garland Avenue, Nashville, TN, 37232, USA
Emailelizabeth.a.scoville@vanderbilt.edu
Phone615-322-5200
Submit Date2017-08-29
Publicationshttps://doi.org/10.1007/s11306-017-1311-y
Analysis Type DetailLC-MS
Release Date2018-01-11
Release Version1
Elizabeth Scoville Elizabeth Scoville
https://dx.doi.org/10.21228/M8W983
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000625
Project DOI:doi: 10.21228/M8W983
Project Title:Alterations in Lipid, Amino Acid, and Energy Metabolism Distinguish Crohn Disease from Ulcerative Colitis and Control Subjects by Serum Metabolomic Profiling
Project Summary:Non-invasive biomarkers are needed in inflammatory bowel disease (IBD) to help define disease activity and identify underlying pathogenic mechanisms. We hypothesized that serum metabolomics, which produces unique metabolite profiles, can aid in this search. The aim of this study was to characterize serum metabolomic profiles in patients with IBD, and to assess for differences between patients with ulcerative colitis (UC), Crohn disease (CD), and non-IBD subjects. Serum samples from 20 UC, 20 CD, and 20 non-IBD control subjects were obtained along with patient characteristics, including medication use and clinical disease activity. Non-targeted metabolomic profiling was performed using ultra-high performance liquid chromatography/mass spectrometry (UPLC-MS/MS) optimized for basic or acidic species and hydrophilic interaction liquid chromatography (HILIC/UPLC-MS/MS).
Institute:Vanderbilt University
Last Name:Scoville
First Name:Elizabeth
Address:1030C MRB IV, 2215 Garland Avenue, Nashville, TN, 37232, USA
Email:elizabeth.a.scoville@vanderbilt.edu
Phone:615-322-5200

Subject:

Subject ID:SU000936
Subject Type:Human serum
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

Subject type: Human serum; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Type
SA05281279Control
SA05281375Control
SA05281473Control
SA05281569Control
SA05281686Control
SA052817121Control
SA0528184Control
SA05281922Control
SA052820144Control
SA05282167Control
SA05282276Control
SA05282343Control
SA05282427Control
SA05282559Control
SA05282650Control
SA05282749Control
SA05282854Control
SA05282951Control
SA05283052Control
SA05283125Control
SA052832318Crohn disease
SA052833321Crohn disease
SA052834324Crohn disease
SA052835313Crohn disease
SA052836303Crohn disease
SA052837327Crohn disease
SA052838305Crohn disease
SA052839306Crohn disease
SA052840309Crohn disease
SA052841310Crohn disease
SA052842304Crohn disease
SA052843342Crohn disease
SA052844345Crohn disease
SA052845347Crohn disease
SA052846341Crohn disease
SA052847337Crohn disease
SA052848330Crohn disease
SA052849333Crohn disease
SA052850335Crohn disease
SA052851329Crohn disease
SA05285288Ulcerative Colitis
SA05285363Ulcerative Colitis
SA05285468Ulcerative Colitis
SA05285571Ulcerative Colitis
SA05285656Ulcerative Colitis
SA05285748Ulcerative Colitis
SA05285812Ulcerative Colitis
SA05285918Ulcerative Colitis
SA05286035Ulcerative Colitis
SA05286177Ulcerative Colitis
SA05286280Ulcerative Colitis
SA052863157Ulcerative Colitis
SA052864168Ulcerative Colitis
SA052865194Ulcerative Colitis
SA052866143Ulcerative Colitis
SA052867130Ulcerative Colitis
SA05286890Ulcerative Colitis
SA05286991Ulcerative Colitis
SA052870125Ulcerative Colitis
SA052871197Ulcerative Colitis
Showing results 1 to 60 of 60

Collection:

Collection ID:CO000930
Collection Summary:Patients with confirmed UC (n = 20) were recruited from either the outpatient endoscopy unit or IBD clinic at Vanderbilt University Medical Center. Patients with confirmed CD (n = 20) were recruited from the IBD clinic at Vanderbilt University Medical Center. IBD diagnosis was determined by accepted clinical and histologic criteria by an IBD specialist. Non-IBD control subjects (n = 20) were recruited from patients undergoing colonoscopy for colorectal cancer screening or other non-IBD related indications. Individuals who were pregnant, had known coagulopathy or bleeding disorders, known renal or hepatic impairment, prior organ transplant, or were unable to give informed consent were excluded. Blood was collected in a vacutainer without additives and allowed to clot. The sample was centrifuged within an hour of collection and serum was aliquoted. Serum samples were snap frozen with dry ice and then stored at –80°C.
Sample Type:Blood

Treatment:

Treatment ID:TR000950
Treatment Summary:Individuals were categorized as either having Crohn disease, Ulcerative colitis, or as non-IBD controls by accepted clinical and histologic criteria by an IBD specialist.

Sample Preparation:

Sampleprep ID:SP000943
Sampleprep Summary:: All samples were maintained at -80oC until processed. Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis.
Sampleprep Protocol Filename:SupplementalMaterial1.docx

Combined analysis:

Analysis ID AN001462 AN001463 AN001464 AN001465
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase HILIC
Chromatography system Waters Acquity Waters Acquity Waters Acquity Waters Acquity
Column Waters Acquity BEH C18 (100 x 2.1mm, 1.7um) Waters Acquity BEH C18 (100 x 2.1mm, 1.7um) Waters Acquity BEH C18 (100 x 2.1mm, 1.7um) Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE NEGATIVE
Units raw area counts raw area counts raw area counts raw area counts

Chromatography:

Chromatography ID:CH001028
Chromatography Summary:One aliquot was analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient-eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). A 2nd aliquot was also analyzed using acidic positive ion conditions, however it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient eluted from the same C18 column using methanol, acetonitrile, water, 0.05% PFPA, and 0.01% FA and was operated at an overall higher organic content. A 3rd aliquot was analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water, however with 6.5mM ammonium bicarbonate at pH 8.
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2.1mm, 1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH001029
Chromatography Summary:The 4th aliquot was analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10mM ammonium formate, pH 10.8.
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Chromatography Type:HILIC

MS:

MS ID:MS001350
Analysis ID:AN001462
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Waters ACQUITY ultra-performance liquid chromatography (UPLC) Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution
Ion Mode:POSITIVE
Resolution Setting:35,000
  
MS ID:MS001351
Analysis ID:AN001463
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Waters ACQUITY ultra-performance liquid chromatography (UPLC) Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution
Ion Mode:POSITIVE
Resolution Setting:35,000
  
MS ID:MS001352
Analysis ID:AN001464
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Waters ACQUITY ultra-performance liquid chromatography (UPLC) Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution
Ion Mode:NEGATIVE
Resolution Setting:35,000
  
MS ID:MS001353
Analysis ID:AN001465
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Waters ACQUITY ultra-performance liquid chromatography (UPLC) Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution
Ion Mode:NEGATIVE
Resolution Setting:35,000
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